It is well known that fluorescence detection provides the basis of flow cytometry, fluorescence imaging, DNA sequencing, microarray detection, drug testing, diagnostics, and so on. It is our goal to extend the power of fluorescence detection in cancer research and diagnostics, by developing new fluorescent probes that absorb and fluoresce in the red and near infrared regions of the spectrum. These advances will: (1) increase the number of parameters that can be acquired in a single experiment (hence, more information becomes available through correlation of cell/tissue properties), (2) increase sensitivity (since cellular autofluorescence is much smaller in the red and near IR), and (3) allow imaging deeper into tissues (since absorbance and fluorescence will be away from hemoglobin absorption and in a range where light scattering and absorption is reduced). The new fluorescent reagents will be photostable, chemically stable, water soluble, brightly fluorescent and non-photo-toxic to cells and tissues. This will be accomplished by synthetic modifications in the molecular structure of cyanine (polymethine) dyes and by stabilizing dye structure through encapsulation methods including cyanine-cyclodextrin rotaxanes, nucleic acid encapsulation, sandwich complexation, and covalent self-encapsulation.